Package picard.vcf.filter
Class FilterApplyingVariantIterator
- java.lang.Object
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- picard.vcf.filter.FilterApplyingVariantIterator
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- All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>
,Closeable
,AutoCloseable
,Iterator<htsjdk.variant.variantcontext.VariantContext>
public class FilterApplyingVariantIterator extends Object implements htsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator. Returns all records from the underlying stream and does not remove any.
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Field Summary
Fields Modifier and Type Field Description static String
ALL_GTS_FILTERED
Filter string that is used to filter a Variant when all variant genotypes are filtered out.static String
PASS_FILTER
The "PASS"ing filter String.
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Constructor Summary
Constructors Constructor Description FilterApplyingVariantIterator(Iterator<htsjdk.variant.variantcontext.VariantContext> iterator, Collection<VariantFilter> filters, Collection<GenotypeFilter> gtFilters)
Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
boolean
hasNext()
htsjdk.variant.variantcontext.VariantContext
next()
Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.void
remove()
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Detail
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ALL_GTS_FILTERED
public static final String ALL_GTS_FILTERED
Filter string that is used to filter a Variant when all variant genotypes are filtered out.- See Also:
- Constant Field Values
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PASS_FILTER
public static final String PASS_FILTER
The "PASS"ing filter String.- See Also:
- Constant Field Values
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Constructor Detail
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FilterApplyingVariantIterator
public FilterApplyingVariantIterator(Iterator<htsjdk.variant.variantcontext.VariantContext> iterator, Collection<VariantFilter> filters, Collection<GenotypeFilter> gtFilters)
Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
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Method Detail
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next
public htsjdk.variant.variantcontext.VariantContext next()
Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
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hasNext
public boolean hasNext()
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close
public void close()
- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfacehtsjdk.samtools.util.CloseableIterator<htsjdk.variant.variantcontext.VariantContext>
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